Topological Data Analysis combined with Machine Learning for Predicting Permeability of Porous Media
Authors: Ebru Dagdelen, Catherin Neena Lalu, Aakash Karlekar, Manav Arora, Matthew Illingworth, Jonathan Jaquette, Linda Cummings, Lou Kondic
Organizations: Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ · Department of Physics, New Jersey Institute of Technology, Newark, NJ
Flow in porous media is difficult to address using standard analytical or numerical methods due to its complexity. However, since synthetic representations of porous media are easy to produce and data from physical experiments are becoming more widely available, the problem is well-suited to studies that include machine learning (ML) techniques. We discuss a number of features that can be extracted from such data, and their utility as input variables into a standard ML algorithm. These features include structural measures describing the geometry of the porous media, topological measures describing the connectivity, and network measures obtained by modeling the porous media as simplified pore networks. These features enable the prediction of the permeability of the considered (synthetic) porous materials using ML techniques that also leverage the separately computed exact permeability (ground truth). Comparing results obtained using different input variables helps develop a better understanding of the utility of various measures for predicting permeability based on the porous media structure. We show, in particular, that topological data analysis (TDA) provides a useful set of features that can be easily combined with ML to yield meaningful results.
Inverse design of three-dimensional porous media is central to applications in filtration, catalysis, energy storage, fuel cells, thermal management, and biomedical scaffolds, but remains challenging because many distinct pore geometries can share similar porosity or permeability while small structural changes can strongly affect transport behaviour. This paper proposes a physics-guided generative AI framework for property-targeted porous media design, combining a property-aware variational autoencoder, a conditional latent diffusion model, and an independently trained differentiable structure-to-property surrogate. The framework learns a compact, physically informative latent design space, generates porous structures conditioned on target porosity and directional permeability, and refines generated samples using property-level feedback during denoising and decoding. Experiments on procedurally generated structures and real micro-CT porous-media datasets show improved target-property matching, directional permeability control, and property correlation compared with representative property-aware variational-autoencoder and latent-diffusion baselines. The results demonstrate a scalable route towards controllable inverse design of complex porous geometries and establish a foundation for simulation-informed generative AI tools in engineering and advanced materials discovery.
We present a unique, multitask dataset comprising 143 drug and drug candidate molecules, each evaluated on in vitro, parallel artificial-membrane permeability assays (PAMPA) using six different model membranes. Using this resource, we systematically assess the effectiveness of various molecular descriptors and regression models in predicting passive membrane permeability. The studied models range from simple linear regression to a modern pre-trained transformer architecture. Particular attention is given to the trade-off between predictive performance and model interpretability, highlighting the challenges introduced by machine learning approaches. To our knowledge, this is the most comprehensive study on simultaneous modeling of multiple organ-specific PAMPA membranes to date, offering novel insights into membrane-specific permeability profiles. We found that expert-designed physico-chemical property descriptors are more fitting for a limited sample size permeabilty study than deep learning based representations.
Diffusion-based voxel prior modelling is challenging for the reconstruction of large-scale 3D porous microstructures. Due to the demanding requirements for simultaneously modelling both the continuous pore morphology and the discrete pore-throat topology, the diffusion models require fully observed CT scans to provide topology-faithful priors, which results in an inherent trade-off among throughput, topological fidelity, and field of view in practical industrial applications. We propose GeoTopoDiff, a graph diffusion-based framework for reconstructing 3D porous microstructures from sparse CT slices. GeoTopoDiff transfers the learning of diffusion priors from a voxel-based space to a mixed graph state space, which simultaneously encompasses continuous pore geometry and discrete pore-throat topology. A topology-aware partial graph prior from sparsely observed CT slices is introduced to constrain the reverse denoising process. Experiments on anisotropic PTFE and Fontainebleau sandstone show that GeoTopoDiff reduces morphology-related errors by 19.8% and topology-sensitive transport errors by 36.5% on average. Our findings suggest that the mixed graph state space promotes the diffusion denoising process to reduce posterior uncertainty under a sparse observations. All models and code have been made publicly available to facilitate the exploration of diffusion models in the field of 3D porous microstructures simulation.